schex

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see schex.

Hexbin plots for single cell omics data

Bioconductor version: 3.13

Builds hexbin plots for variables and dimension reduction stored in single cell omics data such as SingleCellExperiment and SeuratObject. The ideas used in this package are based on the excellent work of Dan Carr, Nicholas Lewin-Koh, Martin Maechler and Thomas Lumley.

Author: Saskia Freytag

Maintainer: Saskia Freytag <saskia.freytag at perkins.uwa.edu.au>

Citation (from within R, enter citation("schex")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("schex")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("schex")

multi_modal_schex HTML R Script

picking_the_right_resolution HTML R Script

Seurat_schex HTML R Script

shiny_schhex HTML R Script

using_schex HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DimensionReduction, Sequencing, SingleCell, Software, Visualization

Version 1.6.3

In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)

License GPL-3

Depends SingleCellExperiment(>= 1.7.4), Seurat, ggplot2 (>= 3.2.1), shiny

Imports hexbin, stats, methods, cluster, dplyr, entropy, ggforce, scales, grid, concaveman

System Requirements

URL https://github.com/SaskiaFreytag/schex

Bug Reports https://github.com/SaskiaFreytag/schex/issues

Suggests ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran

Linking To

Enhances

Depends On Me

Imports Me scTensor, scTGIF

Suggests Me fcoex

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package schex_1.6.3.tar.gz

Windows Binary schex_1.6.3.zip

macOS 10.13 (High Sierra) schex_1.6.3.tgz

Source Repository git clone https://git.bioconductor.org/packages/schex

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/schex

Bioc Package Browser https://code.bioconductor.org/browse/schex/

Package Short Url https://bioconductor.org/packages/schex/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.13 Source Archive